Resource
| Id | DNase-seq/ENCSR943BCO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR943BCO [biosample_summary="Homo sapiens stimulated activated CD8-positive, alpha-beta memory T cell male adult (38 years) treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL Interleukin-4 for 4 hours"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (38 years) treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL Interleukin-4 for 4 hours output_type: peaks audit_warning: Alignment file {ENCFF873RTW|/files/ENCFF873RTW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 28695182 mapped reads. According to ENCODE standards, conventional DNase-seq profile requires a minimum of 20 million uniquely mapped reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million uniquely mapped reads are recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) audit_warning: Signal Portion of Tags (SPOT) is a measure of enrichment, analogous to the commonly used fraction of reads in peaks metric. ENCODE processed alignment files {ENCFF873RTW|/files/ENCFF873RTW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.40. According to ENCODE standards, SPOT1 score of 0.4 or higher is considered a product of high quality data. Any sample with a SPOT1 score <0.3 should be targeted for replacement with a higher quality sample, and a SPOT1 score of 0.25 is considered minimally acceptable SPOT1 score of 0.25 is considered minimally acceptable for rare and hard to find primary tissues. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR943BCO | float |
DNase-seq_ENCSR943BCO |
DNase-seq ENCSR943BCO [biosample_summary="Homo sapiens stimulated activated CD8-positive, alpha-beta memory T cell male adult (38 years) treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL Interleukin-4 for 4 hours"]
|
 |
[0.419, 35.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5559707 | 0.17% | 30077 |
| chr1 | 578165 | 0.23% | 3117 |
| chr2 | 382610 | 0.16% | 2086 |
| chr3 | 302073 | 0.15% | 1633 |
| chr4 | 190189 | 0.10% | 1027 |
| chr5 | 239720 | 0.13% | 1313 |
| chr6 | 319443 | 0.19% | 1730 |
| chr7 | 254679 | 0.16% | 1393 |
| chr8 | 198709 | 0.14% | 1096 |
| chr9 | 226976 | 0.16% | 1212 |
| chr10 | 238595 | 0.18% | 1290 |
| chr11 | 289311 | 0.21% | 1558 |
| chr12 | 290346 | 0.22% | 1555 |
| chr13 | 110686 | 0.10% | 597 |
| chr14 | 193545 | 0.18% | 1044 |
| chr15 | 178473 | 0.17% | 976 |
| chr16 | 234083 | 0.26% | 1269 |
| chr17 | 343875 | 0.41% | 1884 |
| chr18 | 81015 | 0.10% | 443 |
| chr19 | 411855 | 0.70% | 2128 |
| chr20 | 156551 | 0.24% | 888 |
| chr21 | 60349 | 0.13% | 327 |
| chr22 | 133086 | 0.26% | 728 |
| chrX | 140095 | 0.09% | 754 |
| chrY | 5278 | 0.01% | 29 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 30077 | 1 | 700 | 184.85 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF633API.bed.gz | 327.67 KB | 92865062f0931df7403f315cd2faeeb5 |
| ENCFF633API.tabix.bed.gz | 295.76 KB | ebf828596ca88ac6881b537a042ec811 |
| ENCFF633API.tabix.bed.gz.tbi | 174.11 KB | 1a68a5ef0d4929c0b72c1ba61238672d |
| genomic_resource.yaml | 3.27 KB | b8c68b53001a90e4e0a0fc27add07ee9 |
| statistics/ |